[go] 'regulation of gene expression'

[Jim Hu]

I'm relatively new to the group, but I think the term is useful if  
and only if the target (direct or indirect) is specified.  From the  
pov of  an experimentalist, I'd like to mine the annotations to find  
associations that could be pushed down to lower nodes if more data  
was available.  In other words, the ability of GO terms closer to the  
root to identify gaps in the experimental literature is a good thing,  
since it suggests places where more experiments are needed.

A while ago I put up an SF query about whether terms that specify the  
target in the term definition were too specific.  e.g.
GO:0046011 ! regulation of oskar mRNA translation

and it's two children would be lumped into regulation of mRNA  
translation and given oskar mRNA as the target.  It sounds to me like  
the discussion is coming around to my pov on this (I hope?!).  I can  
see why with may not be appropriate, if the regulator is part of a  
complex that does the regulation, then it seems like you could be  
getting into having two kinds of with, the partner and the target.

Adding a new field presumably opens another can of worms, but it  
sounds like maybe one is needed.  But here I'm wading into waters  
best left to more experienced GO people.

Jim

On Aug 10, 2007, at 9:42 AM, E Dimmer wrote:

> Hi,
>
> There is a large number of terms in GO which deserve more  
> information regarding the 'target' of its gene product's activity,  
> for instance:
> -- negative regulation of ubiquitination
> -- protein kinase activity
> -- regulation of DNA binding
> -- regulation of phosphorylation
> -for all of these examples I have information on the specific  
> target of a protein's action.
>
> While I strongly feel that this target information should be  
> captured -- is the 'with' the right place? We seem to have tried to  
> be very strict on the contents of the 'with', so the type of value  
> used is closely related to the type of evidence code applied in the  
> annotation. I'm not sure that regulation of expression be an  
> exception to this...
>
> Emily
>
>
> Pankaj Jaiswal wrote:
>>
>>
>> Harold Drabkin wrote:
>>
>>> Perhaps if used, one needs to restrict the evidence code used  
>>> with it to IEP and perhaps also allow a With field dbx ref for a  
>>> gene_id if known or suspected
>>>
>>
>> With field filling should be 'a must' because the regulation of  
>> expression is always in context to another gene (product). However  
>> the code can also be IPI, IGI, IMP besides IEP.
>>
>> Pankaj
>
>
> -- 
> ************************************
>    Emily Dimmer
>    GOA Coordinator
>    EMBL-EBI
>    Wellcome Trust Genome Campus
>    Hinxton
>    Cambridge CB10 1SD, U.K.
>    Tel:     +44 1223 494654
>    Fax:    +44 1223 494468
>    email:  edimmer at ebi.ac.uk
> ************************************
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054